Genome-wide analysis of SARS-CoV-2 virus strains circulating worldwide implicates heterogeneity

https://www.nature.com/articles/s41598-020-70812-6#Sec2 Article Open Access Published: 19 August 2020 Genome-wide analysis of SARS-CoV-2 virus strains circulating worldwide implicates heterogeneity

Oct 8, Hamilton county to allow big party in restaurant? https://newschannel9.com/news/local/gov-lee-lifts-restrictions-bradley-co-restaurant-calls-executive-order-a-god-send Marl 11, 2020 WHO pandemic declaired.

ARHGAP11B

https://en.wikipedia.org/wiki/ARHGAP11B

computational genomics with R

http://compgenomr.github.io/book/

worldmet

Functions to import data from more than 30,000 surface meteorological sites around the world managed by the National Oceanic and Atmospheric Administration (NOAA) Integrated Surface Database (ISD, see ). https://cran.r-project.org/web/packages/worldmet/index.html https://github.com/davidcarslaw/worldmet Hong note: it seems worldmet only provide pre-defined sites. In Bukhari et al, 2020, effects of weather on coronavirus pandmic, USA weather were provided at the state level. For many other countries, weather were estiamted from the busiest airports.

EpiEstim cran pacakge

https://cran.r-project.org/web/packages/EpiEstim/index.html

EpiNow2 package

https://github.com/epiforecasts/EpiNow2 https://epiforecasts.io/EpiNow2/reference/estimate_infections.html#examples https://github.com/epiforecasts/covid-rt-estimates

These worked

reporting_delay <- bootstrapped_dist_fit(rlnorm(100, log(4), 1), max_value = 30)

generation_time <- get_generation_time(disease = "SARS-CoV-2", source = "ganyani")

incubation_period <- get_incubation_period(disease = "SARS-CoV-2", source = "lauer")

estimates <- epinow(reported_cases = local_cases, samples=100, output='samples',

                    generation_time = generation_time,

                    delays = list(incubation_period, reporting_delay))

localRtTb = estimates$estimates$summarised[ estimates$estimates$summarised$variable=='R' , ]

It seems the default setting is recommended. 

# Note: all examples below have been tuned to reduce the runtimes of examples # these settings are not suggesed for real world use. # run model with default setting

It seems that by default, Rt varies. 

# run model with stationary Rt assumption (likely to provide biased real-time estimates) stat <- estimate_infections(reported_cases, generation_time = generation_time, delays = list(incubation_period, reporting_delay), stan_args = list(warmup = 200, cores = ifelse(interactive(), 4, 1), control = list(adapt_delta = 0.9)), stationary = TRUE)

Rt D3 package

https://epiforecasts.io/RtD3/

possible criteria of a head.

Ability and experience evaluating faculty and staff work performance in an equitable and clearly documented way Ability to communicate with faculty in an open and transparent way Ability to foster an environment in which everyone is comfortable contributing, and in which all voices are considered Ability to unify and support a large, complex, multidisciplinary department that maintains and promotes its disciplinary identities, strengths, and resources Ability to resolve conflict to the advantage of the department as a whole Accessibility and approachability to faculty, staff, and students Commitment and ability to attract and support a diverse and inclusive faculty, staff, and student body Effective advocacy of department needs and promotion of department strengths to upper administration Experience in an administrative role that includes program, budget, and personnel management Motivation and dedication to develop and maintain positive relationships with donors, alumni, and the professional community Support of faculty excellence in teaching across all modalities Support of faculty excellence in research including dissemination and funding Understanding that the department head position is complex, time consuming, and requires total commitment and dedication to the role Other (Please describe any other qualification(s), ability(s), and/or skill(s) that you think should be prioritized in our Department Chair search. Please only describe priorities here that would be among your top five priorities. In other words, priorities that you describe here plus those that you choose from the priorities listed above should amount to no more than five total.)

down load ERA5 land hourly data

 

ERA5 land hours data was last updated on July 12. 

I selected all 2020, all day, and all hours, it is 45.8 GB, which will take 12 hours to download at home.

I ssh into my simcenter workstation, 

wget url, 

which runs with an estimated time of a little over 2 hours. 

Kalman filter versus smoothing splines

 

https://stats.stackexchange.com/questions/15070/kalman-filter-vs-smoothing-splines

beautiful soup

 Beautiful Soup is a Python library for pulling data out of HTML and XML files. It works with your favorite parser to provide idiomatic ways of navigating, searching, and modifying the parse tree. It commonly saves programmers hours or days of work.

https://www.crummy.com/software/BeautifulSoup/bs4/doc/

rvest, websracpping

 

https://blog.rstudio.com/2014/11/24/rvest-easy-web-scraping-with-r/

color in hex values

 

https://www.colorhexa.com/

notes, NSF AI institute meeting


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